9.7. Customisation

Should a large amount of data need to be analysed, then it may make sense to customise some of the Jemboss functions to reduce the amount of time used on certain tasks. This information is stored in the .jembossFavourites file in the home directory and will not be overwritten on installation of a new Jemboss version.

9.7.1. Directory location

On installation of the Jemboss interface (whether as a standalone or client/server option) the software will generally seek out the home directory (Section 9.3.1, “Local File Management”) of the local computer and save all subsequent files to this folder. There is a difference with mEMBOSS in that the home directory will be a subdirectory of the installation directory bearing the user's username. If the folder location is mis-typed, the error message No Access to Directory will appear. Hit the OK button and type the correct location.

Open the local file manager (Section 9.3.1, “Local File Management”) and note the top folder. Typically this will be the username. Access the Preferences menu on the main Jemboss toolbar and select the Advanced Options. Note the location of the local home directory path in the middle of the Advanced Options box and the name of the final folder, it should be the same as the top folder in the Local File Manager (Section 9.3.1, “Local File Management”). Hit the cancel button.

Create a new folder called Extra in the local file manager (Section 9.3.7, “New Folder Creation”). Return to the Advanced Options and enter /Extra (on UNIX) or \Extra (on Windows) at the end of the top folder name and hit the Set button. Hit the Apply button to close the box. The new home directory will automatically be altered in the local file manager.

Re-open the Advanced Options box and hit the Reset button to reset the local home directory to the default setting.

Any directory location on the local computer may be chosen and applied as long as the necessary permissions are in place to allow the user to write to that directory.

The Save between Jemboss Sessions option is selected by default. This selection ensures that the local home directory location is retained between Jemboss sessions. De-selection of this box means that the location is reset to the default after the session. Installation of a new Jemboss version should not alter this selection, unless the selected home directory is the same as the system home directory. This is only an issue for Windows machines, and in this case, the home directory will reset to the default Jemboss home directory.

9.7.2. Programme Selection

The Favourites menu on the main Jemboss toolbar can hold a sizeable number of programs that are used on a regular basis to allow easy selection.

Go to the Protein menu on the left hand side of the Jemboss pane and select the helixturnhelix program from the 2D Structure submenu. Select the Favourites menu from the main Jemboss toolbar and click on the Add to Favourites option. Re-open the Favourites menu and note the new program addition at the bottom of the list.

Programs are added to the list using their one line description with the program name in parentheses.

Select the Favourites/Edit Favourites option and hit the Delete button to the right of the eprimer3 program. Hit the OK button. Re-open the Favourites menu to note the disappearance of eprimer3.

Select the Favourites/Edit Favourites option and alter the helixturnhelix program to antigenic using the alphabetical drop down menu. Delete the helixturnhelix description from the text field to the right of this menu and type Find Antigenic Regions instead. Hit the OK button. Re-open the Favourites menu to note the new program description.

The description of a program does not alter automatically when the program is altered from the drop down menu, so care must be taken to avoid altering one and not the other.

The new list is automatically saved between Jemboss sessions. Once the list has been altered it remains that way and will not automatically return to the original list. The contents of this Favourites list are stored in the .jembossFavorites file on the desktop computer.

9.7.3. Input/Output Options

9.7.3.1. Sequence Input

Should the same sequence be required for analysis by several different programs, it can be set as the default.

Select the Sequence List option from the Tools menu on the main Jemboss toolbar. Left click on the top File/Database Entry field to highlight it, type uni:bgal_ecoli and hit return. The Tools/Get sequence lengths automatically option, when checked, will display the start and end of the sequence (retrieval of this information may take a few seconds). Click with the left hand mouse button on the right hand Default box to select a sequence as the default option. Close the Sequence List window.

All sequence files or USAs may be added to the sequence list. If the added file is a listfile then the Listfile option should be selected. Any number of files may be added to the sequence list, and they can be dragged and dropped into the file input field (Section 9.4.7.1, “File/Database Entry”).

Note that the Get sequence lengths automatically option does not work retrospectively, it must be selected before an entry in the File/Database Entry is made. This option is invalid when the input file is a listfile.

The sequence list will be saved within the same Jemboss session (whether the window is closed or not) and can be saved between Jemboss sessions by selecting the Save Sequence List option from the Tools menu. This creates a .JembossSeqList file on the local computer containing details of the saved list.

9.7.3.2. Adding Sequences

Additional rows in the table can be created using the Tools/Add Sequence option.

9.7.3.3. Deleting Sequences

Rows (empty or full) may be deleted using the Tools/Delete Sequence option. Highlighted rows are deleted individually.

9.7.3.4. Parameter behaviour

Access emma by typing emm into the left hand Go To field and hitting return. Tick the first box under the LOAD SEQUENCE ATTRIBUTES bar to select the Only produce dendrogram file parameter.

This greys out all those parameters which are now no longer required for the analysis run.

Select Preferences and Advanced Settings from the main Jemboss menu and de-select the Shade unused parameters option at the top of the box. Hit Apply.

Place the cursor in the Go To field and hit return to reselect the emma program and reset the parameters. Re-select the Only produce dendrogram file parameter and the unavailable parameters will disappear.

To reset to default, the Advanced Settings must be manually altered.

9.7.3.5. Text Output

All programs that offer a textual output produce results contained in a Text Editor (Section 9.2.9.4, “Text Editors”) window. The view within this window may be altered by changing the size and format of the text using the drop down menus on the toolbar. Use the colour menu to alter the colour of the text and background.

None of these changes can be saved, and they alter the current view only.

9.7.4. Job Manager Update frequency

The Job Manager (Section 9.6.3, “Job Manager”) is set by default to update every 15 seconds. This can be altered in the Preferences/Advanced Options box by selecting an alternative interval from the drop down menu next to the Job Manager Update Frequency option.

9.7.5. Calculate Dependencies

An analysis run depends on the input parameters as well as the sequence attributes and EMBOSS programs will calculate this on the fly for each analysis. De-selecting this option in the Preferences/Advanced Options section allows an analysis to be run without this automatic calculation. This may be useful for testing an analysis and allows the user more control over the workings of the program.

9.7.6. Proxy and Server Settings

To alter the proxies (Section 9.2.11, “Proxies”) and/or server settings, access the Settings options from the Preferences menu on the main Jemboss window.

For the Jemboss standalone version (Section 9.2.5, “Local Installation”) the option is to set a browser proxy. Select the Use proxy settings for HTTP browser connection and type the correct proxy address into the Proxy field. Add the Proxy port number in the second field. Hit the OK button to verify.

For the Jemboss client/server version (Section 9.2.6, “Remote Installation”), both browser proxy and proxy settings can be altered as for the standalone version. In addition, the location for the remote server can be altered by setting the correct name and address for the Public and Private servers. Hit the OK button to verify.